Sodium in PDB 6dbd: Crystal Structure of Vhh R326

The structure of Crystal Structure of Vhh R326, PDB code: 6dbd was solved by C.L.Brooks, M.Toride King, I.Huh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 1.76
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.701, 97.701, 243.800, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 18.2

The binding sites of Sodium atom in the Crystal Structure of Vhh R326 (pdb code 6dbd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Vhh R326, PDB code: 6dbd:

Sodium binding site 1 out of 1 in the Crystal Structure of Vhh R326


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Vhh R326 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:28.2 occ:0.69 OD1 B:ASN83 2.3 34.9 1.0 O B:HOH328 2.3 21.9 1.0 H B:ASN83 3.4 23.9 1.0 CG B:ASN83 3.5 26.9 1.0 HB3 B:ASN82 3.6 22.1 1.0 O B:GLU15 3.8 29.3 1.0 HA B:ASN83 4.0 23.5 1.0 N B:ASN83 4.1 19.9 1.0 HD21 B:ASN83 4.1 36.8 1.0 ND2 B:ASN83 4.3 30.7 1.0 CA B:ASN83 4.4 19.6 1.0 CB B:ASN83 4.6 20.4 1.0 CB B:ASN82 4.6 18.4 1.0 OG B:SER17 4.6 32.8 1.0 HG B:SER17 4.6 39.4 1.0 HB3 B:GLU15 4.7 36.5 1.0 HA B:ASN82 4.9 21.2 1.0 C B:GLU15 5.0 24.1 1.0

M.T.King, I.Huh, A.Shenai, T.M.Brooks, C.L.Brooks. Structural Basis of Vhh-Mediated Neutralization of the Food-Borne Pathogenlisteria Monocytogenes. J. Biol. Chem. V. 293 13626 2018.
ISSN: ESSN 1083-351X
PubMed: 29976754
DOI: 10.1074/JBC.RA118.003888